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- EMDB-16046: The complex of the immature 30S ribosomal subunit with RimP from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16046
TitleThe complex of the immature 30S ribosomal subunit with RimP from S. aureus (body)
Map data
Sample
  • Complex: The complex of immature 30S ribosomal subunit with RimP (body)
KeywordsStaphylococcus aureus / Ribosome / TRANSLATION / RimP
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsGaraeva N / Fatkhullin B / Jenner L / Soufari H / Yusupov M / Usachev K
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-34-70021 Russian Federation
CitationJournal: Structure / Year: 2023
Title: Ribosome maturation factor P (RimP) from Staphylococcus aureus
Authors: Garaeva N / Usachev K
History
DepositionOct 28, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16046.png

Downloads & links

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Map

FileDownload / File: emd_16046.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 384 pix.
= 460.8 Å		1.2 Å/pix.
x 384 pix.
= 460.8 Å		1.2 Å/pix.
x 384 pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.578
Minimum - Maximum-0.87479365 - 3.1832232
Average (Standard dev.)-0.0039170804 (±0.11603675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 460.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16046_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16046_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of immature 30S ribosomal subunit with RimP (body)

EntireName: The complex of immature 30S ribosomal subunit with RimP (body)
Components
  • Complex: The complex of immature 30S ribosomal subunit with RimP (body)

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Supramolecule #1: The complex of immature 30S ribosomal subunit with RimP (body)

SupramoleculeName: The complex of immature 30S ribosomal subunit with RimP (body)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mM/LMgOAcmagnesium acetate
30.0 mM/LNH4ClAmmonium chloride
10.0 mM/LHEPESHEPES
1.0 mM/LDTTDithiothreitol
GridModel: C-flat-2/2 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 3.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 57677
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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